I have some SOLiD data from way back and aligned the reads in colorspace to reference genome my_ref via MosaikAligner. The output of said assembler is a BAM file that, if sorted, indexed (both via samtools) and eventually converted to SAM, exhibits information in colorspace.

I presume that this error is the result of colorspace information contained within the BAM file and that mpileup is unsuccessful due to this circumstance. How would you proceed here?

NOTE 1: Said BAM file can be open and viewed without problem via BamView, which I presume indicates the integrity of the BAM file.

EDIT 1: To clarify my post: I am primarily interested in the question if the inability of 'samtools mpileup' to map the reads against the very reference genome that the reads were aligned to could be the result of the BAM file containing colorspace info, or do I have to consider alternative reasons?